A machine learning framework for predictive interpretation of variants of uncertain significance in hereditary cancer

Variant interpretation remains a major bottleneck in clinical genomics, with variants of uncertain significance (VUS) representing a critical unresolved challenge due to insufficient evidence for definitive classification. Existing in silico tools exhibit variable and often inconsistent performance complicating clinical decision-making, particularly in the context of hereditary cancer genomics.

In this study, we developed a machine learning framework trained on 1,04,646 high-confidence ClinVar germline variants (3-star+ review status) annotated with Ensembl VEP (v114, GRCh38) and CADD v1.6 pathogenicity scores to classify variants as Pathogenic or Benign, subsequently applying the trained model to reclassify 40894 ClinVar VUS. Train/test partitioning was performed at the variant level (80/20 split) to prevent data leakage, with hyperparameter optimization via GridSearchCV and performance assessed by 10-fold cross-validation. Four classifiers were evaluated viz. Logistic Regression, Support Vector Machine, Random Forest and XGBoost, with Random Forest achieving the highest performance (AUC-ROC = 0.9995, 95% CI: 0.9993-0.9997; 10-fold CV AUC = 0.9992 ± 0.0004). Probability thresholds of P ≥ 0.80 (Pathogenic) and P <= 0.20 (Benign) were derived from Precision-Recall curve analysis, achieving empirically validated precision of 99.63% and 99.77% respectively on held-out test variants.

Applied to 40,894 ClinVar VUS, the model reclassified 19393 (47.4%) as Likely Pathogenic and 8,957 (21.9%) as Likely Benign, while 12,544 (30.7%) were conservatively retained as uncertain. External validation on 7,462 ENIGMA-classified BRCA1/BRCA2 variants from the BRCA Exchange database, completely independent of the ClinVar training data demonstrated an overall concordance of 98.83% (AUC = 1.0000). Further validation of VUS reclassification against 671 variants classified as VUS in ClinVar but definitively classified by ENIGMA yielded an overall concordance of 89.57% (Pathogenic: 96.4%, Benign: 87.4%). SHAP-based explainability analysis confirmed that predictions were predominantly driven by biologically interpretable features, including CADD Phred score, VEP functional impact tier, variant consequence class and population allele frequency, consistent with ACMG/AMP evidence criteria. This reproducible pipeline provides a clinically grounded computational approach to VUS triaging in precision oncology, with external validation supporting its generalizability to independent hereditary cancer gene datasets.